library(ggplot2)
library(tidyverse)
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SNPs<- read.table("C:/Users/Zhaozhen Luo/Desktop/2020 spring/bio 497/lab 2/23andMe_complete.txt", header = TRUE, sep = "\t")
chromosome<- ggplot(SNPs, aes(chromosome))
plot_1_1_<- chromosome+geom_bar()
plot_1_2_<- plot_1_1_ + ggtitle("total SNP counts \nof for each chromosome") + labs(y="number of SNPs in each chromosome", x = "chromosome") + geom_bar(fill='steelblue')
plot_1_2_
plot_2_1_<-chromosome + geom_bar(aes(fill=genotype))
plot_2_2_<- plot_2_1_ + scale_fill_manual(values = c("orange", "black", "orange", "orange", "orange", "orange", "black", "orange", "orange", "orange", "green", "green", "orange", "black", "orange", "orange", "green", "green", "black", "orange", "black", "orange", "orange", "black", "orange")) +
ggtitle("Count of Chromosome") + xlab("Chromosome") + ylab("Frequency")
plot_2_2_
plot_4_1_<- chromosome + geom_bar(aes(fill = genotype), position = "dodge") + facet_wrap(~chromosome + genotype)
plot_4_2_<- plot_4_1_ + facet_wrap(~chromosome, scales = "free_x")+ ggtitle("Genotype Contributions of Chromosomes") + xlab("Genotype") + ylab("number of SNPs")
plot_4_2_
library(plotly)
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## layout
table_5_<- ggplotly(
chromosome + geom_bar(aes(fill = genotype), position = "dodge") + facet_wrap(~chromosome + genotype))
table_5_
library(DT)
data_6_ <-subset(SNPs, chromosome=="Y")
datatable(data_6_)
## Warning in instance$preRenderHook(instance): It seems your data is too big
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